#> Loading required package: pacman
CONFIG
countries_of_interest <-
list(
"S. Korea", #"Korea, South",
"Spain",
"Italy" ,
"Norway",
"Israel",
"France",
"Switzerland",
"Sweden",
"Germany",
"Netherlands",
"UK"
)
df <-
read_csv("./data/daily_records_worldmeters.csv") %>%
select(
country = Country,
date = Date,
confirmed = `Total Cases`,
critical = Critical,
recovered = `Total Recovered`,
death = `Total Deaths`
) %>%
mutate(
date = as.Date(date,"%d-%m-%Y"),
) %>%
group_by(country) %>%
arrange(date) %>%
mutate(
active = confirmed - recovered - death,
new_cases = pmax(confirmed - lag(confirmed),0),
r_lag_critical = lag(critical),
r_critical = critical/lag(critical),
r_critical = ifelse(is.infinite(r_critical) | is.nan(r_critical) | is.na(r_critical), 1, r_critical),
r_active = active/lag(active),
r_active = ifelse(is.infinite(r_active) | is.nan(r_active) | is.na(r_active), 1, r_active),
nday = difftime(date, min(date), units = "days") %>% as.integer()
) %>%
ungroup() %>%
arrange(country,date)
#> Parsed with column specification:
#> cols(
#> Date = col_character(),
#> Country = col_character(),
#> `Total Cases` = col_double(),
#> `Total Deaths` = col_double(),
#> `Total Recovered` = col_double(),
#> Critical = col_double()
#> )
tf <-
df %>%
filter(country %in% countries_of_interest) %>%
as_tsibble(key = country, index = date)
# df %>% filter(country == "France") %>% view
data_for_plot <-
tf %>%
group_by(country) %>%
filter(date >= min(date[active>=1])) %>%
mutate(nday = difftime(date, min(date), units = "days") %>% as.integer()) %>%
ungroup()
active & critical vs time (log scale)
data_for_plot %>%
ggplot(aes(x = nday, color = country)) +
geom_line(aes(y = log(critical))) +
geom_line(aes(y = log(active))) +
ylab("active & critical (log scale")+
ggtitle("log(active) & log(critical) vs. time")+
facet_wrap(~country, scales = "free_x")
optimal lag between active and critical
# active slove vs. critical slope: active-lag(active,1) vs. critical-lag(critical
local({
ccf_active_critival_new_cases <-
data_for_plot %>%
update_tsibble(index = nday) %>%
CCF(active-lag(active,1), critical-lag(critical,1))
ccf_active_critival_new_cases %>% autoplot()
ccf_active_critival_new_cases %>%
filter(abs(lag)<=14) %>%
group_by(country) %>%
filter(ccf == max(ccf) & abs(max(ccf))>=0.1) %>%
arrange(desc(ccf)) %>%
mutate(ccf = round(ccf,2))
})
#> # A tsibble: 11 x 3 [1]
#> # Key: country [11]
#> # Groups: country [11]
#> country lag ccf
#> <chr> <lag> <dbl>
#> 1 Italy 3 0.88
#> 2 France -1 0.8
#> 3 Sweden 1 0.71
#> 4 Israel 0 0.69
#> 5 Spain 0 0.59
#> 6 Netherlands -1 0.56
#> 7 Germany -1 0.55
#> 8 Norway -2 0.53
#> 9 UK 2 0.47
#> 10 Switzerland -2 0.38
#> 11 S. Korea -4 0.22
# active r vs. critical r
local({
ccf_active_critival <-
data_for_plot %>%
update_tsibble(index = nday) %>%
CCF(r_active, r_critical)
ccf_active_critival %>%
autoplot()
ccf_active_critival %>%
filter(abs(lag)<=14) %>%
group_by(country) %>%
arrange(desc(ccf)) %>%
mutate(ccf_round = round(ccf,2)) %>%
arrange(lag) %>%
filter(lag<0, ccf>0.1) %>%
pivot_wider(country,names_from=lag,
values_from = ccf_round)
#
# z %>%
# filter(lag<0) %>%
# group_by(country) %>%
# mutate(ccf_normalized = ccf/max(abs(ccf))) %>%
# ungroup() %>%
# ggplot(aes(x=lag, y=country, fill = ccf/ccf_normalized))+
# geom_tile()+
# scale_fill_gradient(low="white", high="blue") +
# theme_ipsum()
})
#> Warning: Current temporal ordering may yield unexpected results.
#> Suggest to sort by `country`, `lag` first.
#> Warning: Current temporal ordering may yield unexpected results.
#> Suggest to sort by `country`, `lag` first.
#> # A tibble: 8 x 14
#> # Groups: country [8]
#> country `-13` `-12` `-11` `-10` `-9` `-8` `-7` `-6` `-5` `-4`
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Spain 0.580 0.33 NA 0.22 NA 0.11 0.13 0.12 NA 0.15
#> 2 Sweden 0.16 0.17 NA NA NA NA NA NA NA NA
#> 3 S. Kor… 0.11 0.24 0.38 0.27 0.24 NA 0.22 0.32 0.3 0.3
#> 4 Israel NA 0.27 NA 0.22 NA 0.23 NA 0.16 NA NA
#> 5 France NA 0.17 NA NA NA NA NA NA NA NA
#> 6 Nether… NA 0.13 NA NA 0.27 NA NA NA NA NA
#> 7 Italy NA NA NA NA NA 0.13 0.2 NA 0.18 NA
#> 8 UK NA NA NA NA NA NA 0.2 NA NA NA
#> # … with 3 more variables: `-3` <dbl>, `-2` <dbl>, `-1` <dbl>
# cdf by optimal lag - note the lag = -12 zon
local({
data_for_plot %>%
update_tsibble(index = nday) %>%
CCF(r_active, r_critical) %>%
arrange(country, lag) %>%
mutate(ccf = round(ccf,2)) %>%
group_by(country) %>%
slice(max(0,which.max(ccf)-3): max(0,which.max(ccf)+3))
})
#> # A tsibble: 66 x 3 [1]
#> # Key: country [11]
#> # Groups: country [11]
#> country lag ccf
#> <chr> <lag> <dbl>
#> 1 France -5 -0.21
#> 2 France -4 -0.03
#> 3 France -3 0.27
#> 4 France -2 0.74
#> 5 France -1 0.1
#> 6 France 0 0.15
#> 7 France 1 0.02
#> 8 Germany -11 -0.02
#> 9 Germany -10 0
#> 10 Germany -9 -0.02
#> # … with 56 more rows
# max lag = -2 ==> active precedes critical by 2.
# tibble(
# day = 1:9,
# active = c( 0, 1, 2,3,-4,-5,6,NA,NA),
# critcal = c(NA, NA,0,1, 2, 3,-4,-5,6)
# ) %>%
# as_tsibble(index = day) %>%
# CCF(active,critcal) %>%
# arrange(desc(ccf))
r_active & r_critical vs time
data_for_plot %>%
ggplot(aes(x = nday)) +
geom_line(aes(y = r_critical, color = "critical")) +
geom_line(aes(y = r_active, color = "active")) +
# ylab("active & critical (log scale")+
ggtitle("active rate & critical rate vs. time")+
ylim(0,2)+
# guides(color=guide_legend(title="patient type - red - critical, green - active")) +
facet_wrap(~country, scales = "free")
% active vs. time
OPT_ACTIVE_CRITICAL_LAG <- 7
tf_enriched <-
tf %>%
update_tsibble(index = nday) %>%
group_by(country) %>%
filter(date >= min(date[active>=1])) %>%
arrange(date) %>%
mutate(r_active_lag = lag(active, OPT_ACTIVE_CRITICAL_LAG),
lag_active = lag(active, OPT_ACTIVE_CRITICAL_LAG),
prc_critical_active_lagged = 100*critical/lag_active,
prc_critical_active_lagged = ifelse(is.infinite(prc_critical_active_lagged) | is.nan(prc_critical_active_lagged) | is.na(prc_critical_active_lagged), 0, prc_critical_active_lagged) %>% pmax(0) %>% pmin(100)
) %>%
ungroup()
(tf_enriched %>%
ggplot(aes(x=nday, y=round(prc_critical_active_lagged,2), color = country)) +
geom_line() +
ggtitle("Convert rate - % critcal out of active (7 day lag)")+
# theme(legend.position='none')+
facet_wrap(~country, scales = "free_x")) %>%
ggplotly